HiCBrowser Compatibility

[matanel-y]

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• [ ] Paste your HiCExplorer version (hicInfo --version) and your python version (python --version) below.

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• [ ] Do you use the latest HiCExplorer release? If not, please install it via a conda environment: conda create --name hicexplorer hicexplorer=3.6 python=3.8 -c bioconda -c conda-forge and activate the environment: conda activate hicexplorer. Retry your command. You can exit a conda environment via conda deactivate. To learn more about conda and environments, please consider the following documentation.

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[joachimwolff]

@LeilyR That's something MPI needs to answer.

[lldelisle]

I remember at one point I tried to make it work but I do not remember where I stopped: https://github.com/lldelisle/HiCBrowser/tree/update

[matanel-y]

So HiCBrowser is not really supported and updated along with HiCExplorer? Are there any plans to keep HiCBrowser going or is it going to be depreciated? If so do you have any recommendations to achieve a similar browsing experience?

[lldelisle]

I would also be in favour of a rescucitation/adaptation of HiCBrowser. In fact HiCBrowser is using a part of HiCExplorer which has slightly detached (pyGenomeTracks), we had in project to support pyGenomeTracks as a package which would, I think, help a lot but this is in standby because we (the developers) have been trapped by different projects. But it is still in my TODO list. As an alternative, I heard about https://github.com/GangCaoLab/CoolBox which diverged from pyGenomeTracks but I never used it. However, since it diverged since a very long time, most of new features of pyGenomeTracks are not included...